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This happens because of a race condition between the scanner discovery and the project getting deleted at the end of a test. If you change the schedule call at the end of org.eclipse.cdt.managedbuilder.language.settings.providers.AbstractBuiltinSpecsDetector.execute() you can reproduce this, or similar problems, quite easily.
To fix it, probably more checks needed in the specs runner to bail out if the project is gone (or the workbench is shutdown)
When running test cases sometimes I see:
Internal error while trying to serialize language settings Resource '/noFilesToBuild' does not exist.
as part of the failing test.
e.g.:
test30NoFilesToBuild (org.eclipse.cdt.managedbuilder.core.tests.ManagedProject30MakefileTests) failed
Follow-on from #117
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